The quantitation of residual leukemia during and after chemotherapy is an important need in the design of improved treatment regimens for acute lymphoblastic leukemia. Specific markers for the leukemic clone have not been generally available. In this proposal, the immunoglobulin heavy chain third hypervariable region (HVR3) gene sequences will be exploited as clonol markers for the leukemic population. These HVR3 segments can be rapidly isolated and sequenced using the polymerase chain reaction (PCR). HVR3 allele-specific oligonucleotides have been prepared and assays constructed which detect 10 leukemic cells in a background of 10 6 normal mononuclear leukocytes. Using these methods, we now propose to develop a quantitative assay for leukemia-specific HVR3 alleles. This assay will be applied to the detection of minimal residual disease in the context of ongoing clinical trials of pediatric and adult ALL patients. A trial will be initiated to test the power of this assay to predict hematologic relapse.